# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 12:20:16 2021
#   Inital geometry file: a 135 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O)N4CC[NH2+]CC4
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 O05  O05  '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-piperazin-4-ium-1-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  59  33  .  2021-08-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_O05
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 O05  C2   C  CR6   0   0.638  -12.3649  24.6487  -36.8052
 O05  C3   C  CH2   0  -1.021  -16.8004  18.0101  -29.3456
 O05  C4   C  CR56  0   0.520  -13.9790  23.2485  -36.2606
 O05  C5   C  CR56  0  -0.057  -14.4649  23.1872  -37.5546
 O05  C6   C  CR6   0   0.471  -13.7815  23.9753  -38.4996
 O05  C8   C  CR15  0   0.100  -15.7159  21.9184  -36.4212
 O05  C9   C  CH2   0  -0.347  -10.9075  25.6273  -35.0934
 O05  C10  C  CH2   0  -0.323  -11.4350  26.9815  -34.6554
 O05  C11  C  CH2   0  -0.323  -11.2159  27.7473  -37.0149
 O05  C12  C  CH2   0  -0.344  -10.7003  26.3651  -37.3711
 O05  O2A  O  O     0  -0.713  -18.3406  19.4384  -31.1201
 O05  PA   P  P     0   1.394  -17.4382  18.2534  -31.0110
 O05  O1A  O  OH1   0  -0.718  -18.1037  16.8427  -31.3393
 O05  PB   P  P     0   1.389  -16.3076  19.5960  -28.6121
 O05  O3B  O  OH1   0  -0.753  -17.6350  20.4777  -28.5978
 O05  O1B  O  O     0  -0.701  -15.1182  20.1891  -29.2816
 O05  O2B  O  OH1   0  -0.722  -16.1576  19.3515  -27.0440
 O05  O5'  O  O2    0  -0.584  -16.1097  18.3470  -31.8900
 O05  C4'  C  CH1   0   0.000  -15.0107  20.2963  -32.7525
 O05  O4'  O  O2    0  -0.498  -14.4393  20.7588  -33.9772
 O05  C3'  C  CH1   0  -0.080  -15.6982  21.5115  -32.1031
 O05  O7   O  OH1   0  -0.695  -14.8648  22.1761  -31.1998
 O05  C2'  C  CH1   0   0.003  -15.9362  22.4021  -33.3224
 O05  O8   O  OH1   0  -0.653  -16.0703  23.7658  -33.0900
 O05  C1'  C  CH1   0   0.203  -14.6776  22.1322  -34.1369
 O05  N9   N  NR5   0  -0.551  -14.7978  22.4308  -35.5345
 O05  N7   N  N     0  -0.446  -15.5504  22.3485  -37.6329
 O05  N6   N  NH2   0  -0.819  -14.1353  24.0221  -39.7847
 O05  N3   N  N     0  -0.526  -12.9447  23.9569  -35.8279
 O05  N1   N  N     0  -0.535  -12.7391  24.6950  -38.0891
 O05  N2   N  NT    0  -0.499  -11.2464  25.3706  -36.4754
 O05  N4   N  NT2   1  -0.645  -10.9274  28.0369  -35.5799
 O05  H19  H  HCH2  0   0.342  -17.5917  17.5697  -28.7346
 O05  H18  H  HCH2  0   0.346  -15.9507  17.3249  -29.3460
 O05  H15  H  HCR5  0   0.290  -16.4843  21.2264  -36.1106
 O05  H13  H  HCH2  0   0.303  -11.3220  24.8590  -34.4482
 O05  H14  H  HCH2  0   0.276   -9.8194  25.5983  -34.9855
 O05  H11  H  HCH2  0   0.310  -11.1052  27.2390  -33.6519
 O05  H12  H  HCH2  0   0.298  -12.5225  27.0186  -34.6955
 O05  H9   H  HCH2  0   0.310  -10.7383  28.5233  -37.6082
 O05  H8   H  HCH2  0   0.298  -12.2955  27.8144  -37.1411
 O05  H7   H  HCH2  0   0.302  -10.9675  26.1418  -38.3989
 O05  H6   H  HCH2  0   0.275   -9.6092  26.3441  -37.2986
 O05  H20  H  HOH1  0   0.505  -18.6910  16.8318  -32.1089
 O05  H21  H  HOH1  0   0.492  -18.1309  20.4144  -29.4385
 O05  H22  H  HOH1  0   0.504  -15.2653  19.1009  -26.7688
 O05  H16  H  HCH2  0   0.240  -16.9005  19.4776  -33.4674
 O05  H17  H  HCH2  0   0.273  -15.4837  18.4849  -33.8208
 O05  H1   H  HCH1  0   0.258  -14.2123  19.9229  -32.1029
 O05  H2   H  HCH1  0   0.242  -16.6497  21.2299  -31.6384
 O05  H23  H  HOH1  0   0.458  -14.8179  21.6047  -30.4141
 O05  H3   H  HCH1  0   0.233  -16.8021  21.9955  -33.8666
 O05  H24  H  HOH1  0   0.463  -16.9044  23.9222  -32.6364
 O05  H    H  HCH1  0   0.261  -13.8446  22.7384  -33.7625
 O05  H5   H  HNH2  0   0.402  -13.6655  24.6462  -40.4175
 O05  H4   H  HNH2  0   0.411  -14.9489  23.5339  -40.1151
 O05  H10  H  HNT2  0   0.467   -9.9205  28.1495  -35.4486
 O05  H25  H  HNT2  0   0.482  -11.3327  28.9377  -35.3254
 O05  C5'  C  CH2   0  -0.209  -15.9405  19.1341  -33.0736

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 O05  N6   C6   single    1.334  0.020  1.334
 O05  C6   N1   aromatic  1.331  0.020  1.331
 O05  C6   C5   aromatic  1.408  0.020  1.408
 O05  N1   C2   aromatic  1.338  0.020  1.338
 O05  N7   C5   aromatic  1.374  0.020  1.374
 O05  N7   C8   aromatic  1.296  0.020  1.296
 O05  C12  C11  single    1.518  0.020  1.518
 O05  C12  N2   single    1.445  0.020  1.445
 O05  C5   C4   aromatic  1.384  0.020  1.384
 O05  C11  N4   single    1.492  0.020  1.492
 O05  C2   N2   single    1.371  0.020  1.371
 O05  C2   N3   aromatic  1.330  0.020  1.330
 O05  C8   N9   aromatic  1.375  0.020  1.375
 O05  N2   C9   single    1.446  0.020  1.446
 O05  C4   N3   aromatic  1.326  0.020  1.326
 O05  C4   N9   aromatic  1.366  0.020  1.366
 O05  N4   C10  single    1.492  0.020  1.492
 O05  N9   C1'  single    1.434  0.020  1.434
 O05  C9   C10  single    1.518  0.020  1.518
 O05  C1'  O4'  single    1.403  0.020  1.403
 O05  C1'  C2'  single    1.523  0.020  1.523
 O05  O4'  C4'  single    1.428  0.020  1.428
 O05  C2'  O8   single    1.390  0.020  1.390
 O05  C2'  C3'  single    1.529  0.020  1.529
 O05  C5'  C4'  single    1.523  0.020  1.523
 O05  C5'  O5'  single    1.431  0.020  1.431
 O05  C4'  C3'  single    1.540  0.020  1.540
 O05  O5'  PA   single    1.596  0.020  1.596
 O05  C3'  O7   single    1.397  0.020  1.397
 O05  O2A  PA   double    1.494  0.020  1.494
 O05  PA   O1A  single    1.594  0.020  1.594
 O05  PA   C3   single    1.800  0.020  1.800
 O05  C3   PB   single    1.815  0.020  1.815
 O05  O1B  PB   double    1.488  0.020  1.488
 O05  PB   O3B  single    1.594  0.020  1.594
 O05  PB   O2B  single    1.594  0.020  1.594
 O05  C3   H19  single    0.970  0.020  1.090
 O05  C3   H18  single    0.970  0.020  1.090
 O05  C8   H15  single    0.930  0.020  1.080
 O05  C9   H13  single    0.970  0.020  1.090
 O05  C9   H14  single    0.970  0.020  1.090
 O05  C10  H11  single    0.970  0.020  1.090
 O05  C10  H12  single    0.970  0.020  1.090
 O05  C11  H9   single    0.970  0.020  1.090
 O05  C11  H8   single    0.970  0.020  1.090
 O05  C12  H7   single    0.970  0.020  1.090
 O05  C12  H6   single    0.970  0.020  1.090
 O05  O1A  H20  single    0.850  0.020  0.980
 O05  O3B  H21  single    0.850  0.020  0.980
 O05  O2B  H22  single    0.850  0.020  0.980
 O05  C5'  H16  single    0.970  0.020  1.090
 O05  C5'  H17  single    0.970  0.020  1.090
 O05  C4'  H1   single    0.970  0.020  1.090
 O05  C3'  H2   single    0.970  0.020  1.090
 O05  O7   H23  single    0.850  0.020  0.980
 O05  C2'  H3   single    0.970  0.020  1.090
 O05  O8   H24  single    0.850  0.020  0.980
 O05  C1'  H    single    0.970  0.020  1.090
 O05  N6   H5   single    0.860  0.020  1.020
 O05  N6   H4   single    0.860  0.020  1.020
 O05  N4   H10  single    0.890  0.020  1.040
 O05  N4   H25  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 O05  N2   C2   N1   116.14  3.000
 O05  N2   C2   N3   116.90  3.000
 O05  N1   C2   N3   126.94  3.000
 O05  H18  C3   H19  108.13  3.000
 O05  H18  C3   PB   109.71  3.000
 O05  H19  C3   PB   108.83  3.000
 O05  H18  C3   PA   111.12  3.000
 O05  H19  C3   PA   108.38  3.000
 O05  PB   C3   PA   110.61  3.000
 O05  N3   C4   N9   127.85  3.000
 O05  N9   C4   C5   105.08  3.000
 O05  N3   C4   C5   127.07  3.000
 O05  N7   C5   C6   133.41  3.000
 O05  N7   C5   C4   110.96  3.000
 O05  C6   C5   C4   115.63  3.000
 O05  N1   C6   N6   119.06  3.000
 O05  N1   C6   C5   118.41  3.000
 O05  N6   C6   C5   122.52  3.000
 O05  H15  C8   N7   124.92  3.000
 O05  H15  C8   N9   121.90  3.000
 O05  N7   C8   N9   113.19  3.000
 O05  H14  C9   H13  107.60  3.000
 O05  H14  C9   N2   108.83  3.000
 O05  H13  C9   N2   110.66  3.000
 O05  H14  C9   C10  109.93  3.000
 O05  H13  C9   C10  109.11  3.000
 O05  N2   C9   C10  110.65  3.000
 O05  H12  C10  H11  109.20  3.000
 O05  H12  C10  N4   107.03  3.000
 O05  H11  C10  N4   107.53  3.000
 O05  H12  C10  C9   111.52  3.000
 O05  H11  C10  C9   111.85  3.000
 O05  N4   C10  C9   109.52  3.000
 O05  H8   C11  H9   109.17  3.000
 O05  H8   C11  N4   106.93  3.000
 O05  H9   C11  N4   107.53  3.000
 O05  H8   C11  C12  111.45  3.000
 O05  H9   C11  C12  111.88  3.000
 O05  N4   C11  C12  109.68  3.000
 O05  H6   C12  H7   107.72  3.000
 O05  H6   C12  N2   108.82  3.000
 O05  H7   C12  N2   110.63  3.000
 O05  H6   C12  C11  109.93  3.000
 O05  H7   C12  C11  109.02  3.000
 O05  N2   C12  C11  110.66  3.000
 O05  O5'  PA   O1A  106.62  3.000
 O05  O1A  PA   O2A  115.78  3.000
 O05  O5'  PA   O2A  114.60  3.000
 O05  O1A  PA   C3   102.65  3.000
 O05  O2A  PA   C3   112.89  3.000
 O05  O5'  PA   C3   102.86  3.000
 O05  H20  O1A  PA   115.28  3.000
 O05  O2B  PB   O1B  115.37  3.000
 O05  O2B  PB   O3B   98.89  3.000
 O05  O1B  PB   O3B  116.70  3.000
 O05  O2B  PB   C3   106.80  3.000
 O05  O3B  PB   C3   105.12  3.000
 O05  O1B  PB   C3   112.54  3.000
 O05  H21  O3B  PB   112.26  3.000
 O05  H22  O2B  PB   114.00  3.000
 O05  C5'  O5'  PA   125.88  3.000
 O05  H1   C4'  C3'  110.15  3.000
 O05  H1   C4'  O4'  109.11  3.000
 O05  C3'  C4'  O4'  106.54  3.000
 O05  H1   C4'  C5'  108.07  3.000
 O05  C3'  C4'  C5'  114.75  3.000
 O05  O4'  C4'  C5'  108.10  3.000
 O05  C1'  O4'  C4'  110.28  3.000
 O05  H2   C3'  C2'  110.66  3.000
 O05  H2   C3'  O7   111.48  3.000
 O05  C2'  C3'  O7   109.35  3.000
 O05  H2   C3'  C4'  111.33  3.000
 O05  O7   C3'  C4'  112.44  3.000
 O05  C2'  C3'  C4'  101.12  3.000
 O05  H23  O7   C3'  105.76  3.000
 O05  H3   C2'  C1'  108.67  3.000
 O05  H3   C2'  O8   111.67  3.000
 O05  C1'  C2'  O8   110.06  3.000
 O05  H3   C2'  C3'  107.56  3.000
 O05  O8   C2'  C3'  116.96  3.000
 O05  C1'  C2'  C3'  101.23  3.000
 O05  H24  O8   C2'  108.78  3.000
 O05  H    C1'  N9   106.34  3.000
 O05  H    C1'  C2'  110.32  3.000
 O05  N9   C1'  C2'  114.52  3.000
 O05  H    C1'  O4'  111.92  3.000
 O05  C2'  C1'  O4'  104.65  3.000
 O05  N9   C1'  O4'  109.20  3.000
 O05  C1'  N9   C8   127.35  3.000
 O05  C1'  N9   C4   126.33  3.000
 O05  C8   N9   C4   106.28  3.000
 O05  C8   N7   C5   104.49  3.000
 O05  H4   N6   H5   118.24  3.000
 O05  H4   N6   C6   120.97  3.000
 O05  H5   N6   C6   120.28  3.000
 O05  C4   N3   C2   112.20  3.000
 O05  C6   N1   C2   119.74  3.000
 O05  C12  N2   C9   112.43  3.000
 O05  C9   N2   C2   120.96  3.000
 O05  C12  N2   C2   121.42  3.000
 O05  H25  N4   H10  105.20  3.000
 O05  H25  N4   C11  109.54  3.000
 O05  H10  N4   C11  109.61  3.000
 O05  H25  N4   C10  109.57  3.000
 O05  H10  N4   C10  109.49  3.000
 O05  C11  N4   C10  113.13  3.000
 O05  H17  C5'  H16  107.95  3.000
 O05  H17  C5'  C4'  110.07  3.000
 O05  H16  C5'  C4'  111.87  3.000
 O05  H17  C5'  O5'  106.79  3.000
 O05  H16  C5'  O5'  111.52  3.000
 O05  C4'  C5'  O5'  108.51  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 O05  CONST_01  C5   C6   N1   C2     0.00   0.0  0
 O05  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 O05  CONST_03  N9   C4   N3   C2   180.00   0.0  0
 O05  CONST_04  N1   C6   C5   C4     0.00   0.0  0
 O05  CONST_05  C8   N7   C5   C4     0.00   0.0  0
 O05  CONST_06  N1   C2   N3   C4     0.00   0.0  0
 O05  CONST_07  N7   C8   N9   C4     0.00   0.0  0
 O05  CONST_08  N9   C8   N7   C5     0.00   0.0  0
 O05  CONST_09  C8   N9   C4   C5     0.00   0.0  0
 O05  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 O05  CONST_11  C8   N7   C5   C6   180.00   0.0  0
 O05  CONST_12  N3   C4   C5   C6     0.00   0.0  0
 O05  CONST_13  N9   C4   C5   C6   180.00   0.0  0
 O05  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 O05  CONST_15  N7   C5   C4   N9     0.00   0.0  0
 O05  CONST_16  N1   C6   C5   N7   180.00   0.0  0
 O05  CONST_17  N3   C4   C5   N7   180.00   0.0  0
 O05  CONST_18  N2   C2   N3   C4   180.00   0.0  0
 O05  CONST_19  C1'  N9   C4   C5   180.00   0.0  0
 O05  CONST_20  N2   C2   N1   C6   180.00   0.0  0
 O05  CONST_21  N7   C8   N9   C1'  180.00   0.0  0
 O05  CONST_22  N3   C4   N9   C1'    0.00   0.0  0
 O05  CONST_23  N6   C6   N1   C2   180.00   0.0  0
 O05  CONST_24  N6   C6   C5   C4   180.00   0.0  0
 O05  CONST_25  N6   C6   C5   N7     0.00   0.0  0
 O05  CONST_26  H15  C8   N9   C4   180.00   0.0  0
 O05  CONST_27  H5   N6   C6   C5   180.00   0.0  0
 O05  CONST_28  H4   N6   C6   C5     0.00   0.0  0
 O05  Var_01    C11  C12  N2   C2    95.37  30.0  1
 O05  Var_02    C10  C9   N2   C2   -95.30  30.0  1
 O05  Var_03    N1   C2   N2   C9   166.91  30.0  2
 O05  Var_04    C11  N4   C10  C9    53.57  30.0  1
 O05  Var_05    C12  C11  N4   C10  -53.46  30.0  1
 O05  Var_06    N4   C11  C12  N2    54.78  30.0  1
 O05  Var_07    N4   C10  C9   N2   -55.09  30.0  1
 O05  Var_08    C4'  C5'  O5'  PA   109.06  30.0  1
 O05  Var_09    PB   C3   PA   O2A  -42.43  30.0  3
 O05  Var_10    O1B  PB   C3   PA   -68.15  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 O05  chir_02  C4'  O4'  C5'  C3'  positiv
 O05  chir_03  C3'  O7   C4'  C2'  positiv
 O05  chir_04  C2'  O8   C3'  C1'  positiv
 O05  chir_05  C1'  O4'  N9   C2'  negativ
 O05  chir_06  PA   O2A  O1A  C3   both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 O05  plan-1  C6   0.020
 O05  plan-1  N6   0.020
 O05  plan-1  H5   0.020
 O05  plan-1  H4   0.020
 O05  plan-2  C2   0.020
 O05  plan-2  C4   0.020
 O05  plan-2  C5   0.020
 O05  plan-2  C6   0.020
 O05  plan-2  C8   0.020
 O05  plan-2  C1'  0.020
 O05  plan-2  N9   0.020
 O05  plan-2  N7   0.020
 O05  plan-2  N6   0.020
 O05  plan-2  N3   0.020
 O05  plan-2  N1   0.020
 O05  plan-2  N2   0.020
 O05  plan-2  H15  0.020

